• DATA
  • LOCATIONS
  • IDS
  • HUMAN

How to map proteins to genomic coordinates with your AI

Connect the EBI Proteins API to your agent to bridge the gap between protein data and genomic locations. Once connected, your AI handles the lookups for you.

Ask AI about this page

Short answer

How do I map protein sequences to genomic coordinates?

Your AI uses the EBI Proteins API to find specific protein records and then pulls the corresponding chromosome positions and Ensembl IDs. You get a direct link between sequence annotations and their exact genomic locations.

Mapping outcomes

Where your data lands

The AI handles the heavy lifting of data retrieval and coordinate matching.

DATA

Protein identification

The AI finds specific protein records using sequence or name searches. You get the raw annotations needed for mapping.

LOCATIONS

Genomic mapping

The AI pulls exact chromosome positions for the identified proteins. This links your sequence data to specific genomic coordinates.

IDS

Ensembl ID linking

The AI retrieves Ensembl IDs to ensure your data stays consistent with standard genomic databases.

HUMAN

Manual verification

You review the final coordinate mappings to ensure they match your specific research context or assembly version.

The workflow

What your AI does when the request arrives.

The AI moves from broad protein searches to specific coordinate lookups.

  1. Find the protein

    The AI searches the EBI database to locate the specific protein sequence or record you are interested in.

    search_proteins

  2. Retrieve details

    The AI pulls the full annotation and sequence information for the identified protein.

    get_protein

  3. Locate coordinates

    The AI finds the exact chromosome position and genomic location for that protein.

    get_coordinates

  4. Map to Ensembl

    The AI links the protein data to the correct Ensembl IDs for your genomic analysis.

    get_coordinates

Try it

Copy these to start.

Use these prompts to trigger the mapping process.

Starting points

Replace the protein names and IDs with your actual research targets.

EMBL-EBI Proteins API Connector

You're all set. Choose your MCP client and follow the setup instructions.

Connector linkhttps://edge.vinkius.com/vk_preview_3jKiKjDDYj38o3vJ2cr3PVaRBrqDRzHtZH05tPSn/mcp

Claude Desktop

Follow the steps below to connect in seconds.

  1. 1In Claude Desktop, open Settings → Connectors.
  2. 2Click “Add custom connector” and paste the connector link above as the remote MCP server URL.
  3. 3Click Add and start a new chat — EMBL-EBI Proteins API capabilities are ready to use.
Configuration · claude_desktop_config.jsonCopy
{
  "mcpServers": {
    "ebi-proteins-api-mcp": {
      "url": "https://edge.vinkius.com/vk_preview_3jKiKjDDYj38o3vJ2cr3PVaRBrqDRzHtZH05tPSn/mcp"
    }
  }
}
Copy into chat04

  • Search for the protein sequence of BRCA1 and find its genomic coordinates.

  • Get the Ensembl ID and chromosome position for the protein with ID P04637.

  • Map the protein sequence for insulin to its exact location on the genome.

  • Find the genomic coordinates for the protein associated with the Ensembl ID ENSG00000139618.

  • Claude
  • ChatGPT
  • Cursor
  • VS Code
  • Windsurf
  • Claude Code
  • JetBrains
  • Cline

Start here

Connect EBI Proteins API once, then ask.

One connection gives your AI access to the EBI database. Your credentials stay encrypted and secure.

Connect EBI Proteins API to your AI

FAQ

How this task behaves

  • 01

    Can the AI edit protein annotations in the EBI database?

    No. The AI can only read and retrieve data from the API.

  • 02

    Does the AI provide the actual DNA sequence?

    Yes, it can retrieve protein sequence information through the protein lookup tool.

  • 03

    Can the AI perform custom genomic alignments?

    No. The AI retrieves existing coordinates from the API but does not run its own alignment algorithms.

  • 04

    Will the AI automatically update my local files with these coordinates?

    No. The AI provides the data in the chat, and you decide how to use it in your own files.

  • 05

    Can I search for proteins by name?

    Yes, the AI uses search tools to find proteins based on names or identifiers.

  • More questions about EBI Proteins API? The Connector page answers them. See everything the EBI Proteins API Connector can do

Connect EMBL-EBI Proteins API to Claude, Cursor, ChatGPT & more